1 Overall

1.1 Plot

1.2 Table

2 Individual metrics

2.1 Overall

2.2 Batch correction

Batch correction

PCR batch

Batch ASW

Graph iLISI

Graph connectivity

kBET

2.3 Bio conservation

Bio conservation

NMI cluster/label

ARI cluster/label

Label ASW

Isolated label F1

Isolated label silhouette

Graph cLISI

HVG conservation

Cell cycle conservation

Trajectory conservation

3 UMAPs

Full

Scaled

MNN - Features

Batch

Labels

Scanorama - Embedding

Batch

Labels

Scanorama - Features

Batch

Labels

Seurat v3 - Features

Batch

Labels

Harmony - Embedding

Batch

Labels

BBKNN - Graph

Batch

Labels

ComBat - Features

Batch

Labels

FastMNN - Embedding

Batch

Labels

FastMNN - Features

Batch

Labels

Unscaled

MNN - Features

Batch

Labels

Scanorama - Embedding

Batch

Labels

Scanorama - Features

Batch

Labels

Seurat v3 - Features

Batch

Labels

Harmony - Embedding

Batch

Labels

BBKNN - Graph

Batch

Labels

scVI - Embedding

Batch

Labels

ComBat - Features

Batch

Labels

LIGER - Embedding

Batch

Labels

scANVI - Embedding

Batch

Labels

FastMNN - Embedding

Batch

Labels

FastMNN - Features

Batch

Labels

Unintegrated - Features

Batch

Labels

HVG

Scaled

MNN - Features

Batch

Labels

Scanorama - Embedding

Batch

Labels

Scanorama - Features

Batch

Labels

Seurat v3 - Features

Batch

Labels

Harmony - Embedding

Batch

Labels

BBKNN - Graph

Batch

Labels

ComBat - Features

Batch

Labels

FastMNN - Embedding

Batch

Labels

FastMNN - Features

Batch

Labels

Unscaled

MNN - Features

Batch

Labels

Scanorama - Embedding

Batch

Labels

Scanorama - Features

Batch

Labels

Seurat v3 - Features

Batch

Labels

Harmony - Embedding

Batch

Labels

BBKNN - Graph

Batch

Labels

scVI - Embedding

Batch

Labels

ComBat - Features

Batch

Labels

LIGER - Embedding

Batch

Labels

scANVI - Embedding

Batch

Labels

FastMNN - Embedding

Batch

Labels

FastMNN - Features

Batch

Labels